[buster-discuss] Beryllium ion refinement

Clayton, Gina ClaytonG at NJHealth.org
Fri Aug 31 20:34:42 CEST 2012

Great than you Oliver!

I will give it a try.


On Aug 31, 2012, at 12:08 PM, Oliver Smart wrote:

> On Fri, 31 Aug 2012, Clayton, Gina wrote:
>>> I have an unusual ion in my structure - a Be2+ ion (at least 1). It is 
>>> surrounded by acidic residues which should be tetrahedral in 
>>> arrangement and are more or less in that position without the ion 
>>> modeled. I am wondering how I can best refine this ion in BUSTER.
>>> Be2+ forms partially covalent complexes with short distances, for 
>>> example BeFl4 distance to each Fl is aprox 1.5Ang. I am guessing I have 
>>> something of this nature in the structure but restrained by the side 
>>> chains themselves i.e. not free oxides.  I have the Be ion defined as 
>>> given by my buster log file - which told me how to define the ion. 
>>> However refinement moves the Be ion out of the +ve density peak into a 
>>> zero density area.
>>> Do you have any ideas how I can specify this ion and at all?
> Gina,
> Please find attached a pdf that shows how a Be2+ ion with contacts to
> acidic residues should be handled. There is a corrected contact.dat
> and an example Gelly file.
> If anything is unclear please let us know.
> Thanks
> Oliver
> | Dr Oliver Smart                             |
> | Global Phasing Ltd., Cambridge UK           |
> | http://www.globalphasing.com/people/osmart/ |
> <OliverSmart2012x08BerylliumIon.pdf><contact_correct_BE.dat><3m4c_be_control_coordination.Gelly><just_a_be2plusion.pdb>

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